The authors present a new method for searching low free energy paths in complex molecular systems at finite temperature. They introduce two variables that are able to describe the position of a point in configurational space relative to a preassigned path. With the help of these two variables the authors combine features of approaches such as metadynamics or umbrella sampling with those of path based methods. This allows global searches in the space of paths to be performed and a new variational principle for the determination of low free energy paths to be established. Contrary to metadynamics or umbrella sampling the path can be described by an arbitrary large number of variables, still the energy profile along the path can be calculated. The authors exemplify the method numerically by studying the conformational changes of alanine dipeptide.
REFERENCES
1.
H.
Jonsson
, G.
Mills
, and K. W.
Jacobsen
, Classical Dynamics in Condensed Phase Simulations
, edited by B. J.
Berne
, G.
Ciccotti
, and D. F.
Coker
(World Scientific
, Singapore
, 1998
), p. 385.2.
G.
Henkelman
and H.
Jonsson
, J. Chem. Phys.
113
, 9978
(2000
).3.
G.
Henkelman
, B. P.
Uberuaga
, and H.
Jonsson
, J. Chem. Phys.
113
, 9901
(2000
).4.
5.
P. G.
Bolhuis
, C.
Dellago
, and D.
Chandler
, Faraday Discuss.
110
, 421
(1998
).6.
P. G.
Bolhuis
, D.
Chandler
, C.
Dellago
, and P. L.
Geissler
, Annu. Rev. Phys. Chem.
53
, 291
(2002
).7.
D.
Passerone
and M.
Parrinello
, Phys. Rev. Lett.
87
, 108302
(2001
).8.
D.
Passerone
, M.
Ceccarelli
, and M.
Parrinello
, J. Chem. Phys.
118
, 2025
(2003
).9.
A. K.
Faradjian
and R.
Elber
, J. Chem. Phys.
120
, 10880
(2004
).10.
E. A.
Carter
, G.
Ciccotti
, J. T.
Hynes
, and R.
Kapral
, Chem. Phys. Lett.
156
, 472
(1989
).11.
M.
Sprik
and G.
Ciccotti
, J. Chem. Phys.
109
, 7737
(1998
).12.
G. N.
Patey
and J. P.
Valleau
, J. Chem. Phys.
63
, 2334
(1975
).13.
A. M.
Ferrenberg
and R. H.
Swendsen
, Phys. Rev. Lett.
61
, 2635
(1988
).14.
S.
Kumar
, J. M.
Rosenberg
, D.
Bouzida
, R. H.
Swendsen
, and P. A.
Kollman
, J. Comput. Chem.
16
, 1339
(1995
).15.
B.
Roux
, Comput. Phys. Commun.
91
, 275
(1995
).16.
C.
Jarzynski
, Phys. Rev. Lett.
78
, 2690
(1997
).17.
E.
Darve
and A.
Pohorille
, J. Chem. Phys.
115
, 9169
(2001
).18.
H.
Grubmüller
, Phys. Rev. E
52
, 2893
(1995
).19.
F. A.
Voter
, Phys. Rev. Lett.
78
, 3908
(1997
).20.
D.
Cvijovic
and J.
Klinowski
, Science
267
, 664
(1995
).21.
T.
Huber
, A. E.
Torda
, and W. F.
van Gunsteren
, J. Comput.-Aided Mol. Des.
8
, 695
(1994
).22.
A.
Laio
and M.
Parrinello
, Proc. Natl. Acad. Sci. U.S.A.
20
, 12562
(2002
).23.
B.
Ensing
, A.
Laio
, M.
Parrinello
, and M. L.
Klein
, J. Phys. Chem. B
109
, 6676
(2005
).24.
B.
Ensing
and M. L.
Klein
, Proc. Natl. Acad. Sci. U.S.A.
102
, 6755
(2005
).25.
L.
Maragliano
, A.
Fischer
, and E.
Vanden-Eijnden
, J. Chem. Phys.
125
, 024106
(2006
).26.
P. J.
Steinhardt
, D. R.
Nelson
, and M.
Ronchetti
, Phys. Rev. Lett.
47
, 1297
(1981
).27.
M.
Iannuzzi
, A.
Laio
, and M.
Parrinello
, Phys. Rev. Lett.
90
, 238302
(2003
).28.
W.
E
, W.
Ren
, and E.
Vanden-Eijnden
, J. Appl. Phys.
93
, 2275
(2003
).29.
D. H.
Mathews
and D. A.
Case
, J. Mol. Biol.
357
, 1683
(2006
).30.
M. R.
Sorensen
, M.
Brandbyge
, and K.
Jacobsen
, Phys. Rev. B
57
, 3283
(1998
).31.
W.
E
, W.
Ren
, and E.
Vanden-Eijnden
, J. Phys. Chem. B
109
, 6688
(2005
).32.
W.
Ren
, E.
Vanden-Eijnden
, P.
Maragakis
, and W.
E
, J. Chem. Phys.
123
, 134109
(2005
).33.
D.
Moroni
, P. G.
Bolhuis
, and T. S.
van Erp
, J. Chem. Phys.
120
, 4055
(2004
).34.
C.
Bartels
and M.
Karplus
, J. Comput. Chem.
18
, 1450
(1997
).35.
J.
Apostolakis
, P.
Ferrara
, and A.
Caflisch
, J. Chem. Phys.
110
, 2099
(1999
).36.
T.
Lazaridis
, D. J.
Tobias
, C. L.
Brooks
, and M. E.
Paulaitis
, J. Chem. Phys.
95
, 7612
(1991
).37.
A.
Laio
, A.
Fortea-Rodriguez
, F. L.
Gervasio
, M.
Ceccarelli
, and M.
Parrinello
, J. Phys. Chem. B
109
, 6714
(2005
).38.
P.
Raiteri
, A.
Laio
, F. L.
Gervasio
, C.
Micheletti
, and M.
Parrinello
, J. Phys. Chem. B
110
, 3533
(2006
).39.
S. K.
Kearsley
, Acta Crystallogr., Sect. A: Found. Crystallogr.
45
, 208
(1989
).40.
P. G.
Bolhuis
, C.
Dellago
, and D.
Chandler
, Proc. Natl. Acad. Sci. U.S.A.
97
, 5877
(2000
).41.
R.
Crehuet
and M. J.
Field
, J. Chem. Phys.
118
, 9563
(2003
).42.
A.
Ma
and A. R.
Dinner
, J. Phys. Chem. B
109
, 6769
(2005
).43.
G. N.
Ramachandran
, C.
Ramakrishnan
, and V.
Sasisekharan
, J. Mol. Biol.
7
, 95
(1963
).44.
A. D.
MacKerell
, Jr., D.
Bashford
, M.
Bellott
et al, J. Phys. Chem. B
102
, 3586
(1998
).45.
P.
Procacci
, T. A.
Darden
, E.
Paci
, and M.
Marchi
, J. Comput. Chem.
18
, 1848
(1997
).46.
M.
Gerstein
and W.
Krebs
, Nucleic Acids Res.
26
, 4280
(1998
).47.
C. W.
Gear
, I. G.
Kevrekidis
, and C.
Theodoropoulos
, Comput. Chem. Eng.
26
, 941
(2002
).48.
G.
Bussi
, A.
Laio
, and M.
Parrinello
, Phys. Rev. Lett.
96
, 090601
(2006
).49.
P. E.
Smith
, J. Chem. Phys.
111
, 5568
(1999
).50.
51.
W.
E
and E.
Vanden-Eijnden
, Multiscale Modelling and Simulation
, edited by S.
Attinger
and P.
Komoutsakos
(Springer
, New York
, 2004
).© 2007 American Institute of Physics.
2007
American Institute of Physics
You do not currently have access to this content.
